There You'll be
by johnliz4ever
Summary: The members of Atlantis have been recalled. Elizabeth reflects on her time with John. JohnLiz


Disclaimer: I don't own Stargate Atlantis or the lyrics to 'There you'll be'

Note: I was listening to Faith Hill and this song and an idea just popped into my head.

Spoilers: All of season 1 Stargate Atlantis. This contains some major spoilers for the last two episodes of the season. Since I haven't seen them I cannot be sure what exactly happens, all it contains is my ideas for what** may **happen.

* * *

It was over. It was all over. The expedition had been annulled. They weren't going back to Atlantis. All the expedition members were being recalled back to Earth. It was over. 

Liz stood at the bottom of the ramp that led to the Stargate. The SGC was different to what she remembered things had changed. That was expected. They'd been on Atlantis for eight years. Things had changed.

Earth seemed loud and crowded. Elizabeth didn't like it. She wanted to go home. To Atlantis.

Simon had got married. She wasn't angry. She was happy for him, but now she was alone.

Elizabeth's thoughts drifted to John. He was just as uncomfortable with the recall of the Atlantis team as she was. She didn't know where John was. He told her he was going to look up some friends.

Elizabeth smiled; John had been a blessing in disguise. She remembered when she asked him to go on the expedition

**:Flashback:**

John stood carefully from the command chair still pretty freaked by what he'd done.

Elizabeth walked to his side as the others around him dispersed.

"Major Sheppard?"

John turned and was faced by Elizabeth

"Major Sheppard, I'm Dr Elizabeth Weir"

The two of them shook hands

"I didn't…" He looked back towards the chair "…compromise anything did I?"

Elizabeth smiled

"No Major, don't worry…" Elizabeth decided to bite the bullet.

"Look Major I'm going to be blunt with you. You have something called the ATA gene. It…"

John nodded

"I know the Scottish doctor told me."

"Okay, there's an expedition, to another planet, in another galaxy which we'll go to by the means of the Stargate. The Stargate is…"

"I know. The Scottish doctor again."

"Here's the facts. There's only an handful of people with this gene. This gene activates certain technology. The others that have it will be able to master it eventually but it will require training. You do it naturally, something we haven't come across yet. What I'm asking is that you come with us on this expedition."

"What?"

"Major, this will be greatly beneficial to mankind, but the chances are we'll never be able to return to Earth."

"You see Dr Weir, that's the problem."

"Major, I've seen your file. I know that they put you in the place where could cause the least amount of trouble. Major the opportunity I'm offering is a once in a lifetime one, and it'll get you out of Antarctica."

Elizabeth could see that John was deciding whether the trip was worth it.

"I'll think about it"

Elizabeth smiled.

"That's all I ask."

John watched as Elizabeth turned round a corner and met up with General O'Neill.

**:End of Flashback:**

Elizabeth smiled at the memory. John had looked so scared when he had activated the command chair but she remembered the small glint in his eyes which made her agree to go and see him at the barracks the next day at McMurdo.

**:Flashback:**

Elizabeth watched as John took a smooth landing. She thought he was very cocky and trying to show off. John exited the plane and walked over to Elizabeth wearing the half-grin that made so many women feel weak at the knees Elizabeth just smirked.

John was slightly surprised. He was also glad he was wearing sunglasses otherwise; she would have seen the surprise in his eyes.

"Dr Weir."

"Major"

John stood in front of her.

"Sorry to call you out here like this."

"It's okay, what can I do for you?"

"We better go somewhere more private."

Elizabeth followed John until they were in an unpopulated part of McMurdo.

John took a seat and Elizabeth followed suit and sat opposite him.

"Okay Dr Weir…"

"Elizabeth, call me Elizabeth."

John nodded

"Call me John then…"

The two shared a smile before John started again

"So _Elizabeth _about this expedition…"

John was sure to speak in a hushed tone.

"…I've told General O'Neill yes but, I wanted to talk to you about it."

Elizabeth smiled

"What would you like to know?"

John cleared his throat.

"I guess first it's who the Military commander is. I know it's your expedition but I'm assuming you'll have Military."

"Colonel Marshall Sumner. You'd actually be second in command to him."

John smirked

"Colonel Sumner?"

"You know him?"

John smirked again

"He'd be less the thrilled at my participation."

Elizabeth smiled at him

"It's not his decision."

The two of them continued to talk for a few more hours before John flew Elizabeth back to the research base.

"Thanks for going through this with me."

Elizabeth began to exit the Chopper.

"So is it a definite 'Yes'."

John smiled nervously

"Yes."

Elizabeth smiled at him.

"Glad to hear it."

**:End of Flashback:  
**

She knew that John had his doubts even after that but he came and that was what mattered.

Elizabeth stared at the Stargate, so many times, she'd sent teams out, some of which never came back. John was always there for her. Always reassuring her always, telling her she'd made the right decision. He gave her strength. He was wiling to go against the Military for her.

**:Flashback:**

The team passed through the Stargate and walked to Dr Weir.

"Dr Weir?"

Elizabeth nodded

"I'm Colonel Mark Westen."

"It's actually a shock that Earth managed to contact us."

"Well I have more of a shock for you Dr Weir. You're being pulled as commander of this mission"

John who was standing behind Elizabeth stepped forward

"What? That's crazy."

"That's what's been ordered Major."

"Sorry you just can't come in here and take command of an expedition that you know nothing about. You don't know what the threat is out there"

"That's why we are here Major. The Pentagon believes that Dr Weir does not have the training to deal with such a threat."

"That…"

John stopped when he felt a hand on his arm; he turned and saw Elizabeth

"It's okay John."

"No way. I won't…"

Elizabeth sighed

"I'll make it easy. I'm ordering you to follow Colonel Westen's orders. Also, I resign from my post as commander."

She looked at Colonel Westen then John before walking away. John started to go after her but the Colonel stopped him

"I suggest you follow her order. Get all the personal together. I'm calling a briefing."

John bit his lip to keep from saying what he was thinking

"Yes Sir." He answered through gritted teeth.

**:End of Flashback:**

Elizabeth remembered the bloodbath that had ensued when the Wraith had attacked. Half of the Military team that had come with Colonel Westen had died including the Colonel himself. That left John in charge since he was Second in command and his first official business was to give the post back to Elizabeth.

John had taken Elizabeth up in a Jumper to survey the area after the attack. He told her there that he was giving her back her position. That no-one other then her was able to do that job. Elizabeth wasn't surprised, she knew John wouldn't want to be in charge.

**:Flashback:**

"I'm giving you your post back."

"What?"

John turned slightly and looked at her

"You're the best person for the job, I'm might be a Military commander but I can't command a whole city. It's not me. Plus the scientists want you back"

Elizabeth smiled

"What about the Military personal?"

"They actually want you back in command. Ford said your better at it."

**:End of Flashback:**

Elizabeth smiled at the memory. He was actually telling the truth. Most of the Military wanted her back in command.

Elizabeth was distracted by a hand, which brushed her back. John stood next to her

"Hi"

Elizabeth looked at him.

"Thought you went to see some friends?"

John smirked

"You know I did set off to find me friends when I realised that my best friend was all alone here."

Elizabeth smiled

"And who is that?"

"I'll give you a clue, she's beautiful, she's my boss and she's the reason I'm still alive."

Elizabeth smiled at him.

"How's Ford?"

"He's a bit nervous; he's taking Teyla to meet his parents."

Elizabeth sighed. The recall had cause Teyla to make a difficult decision. Ford or her people, Teyla eventually decided to come to Earth with Ford. She was upset that she was no longer with her people but hopeful that her people would be okay.

"How's Teyla?"

"Still a little upset, she'll be fine."

The two stood at the bottom of the ramp for a few moments

"Wanna get a drink?"

Elizabeth nodded

"Yeah."

The two left the 'gate room. John placed his arm around Elizabeth shoulders as she took one last look into the gate room. Then she looked into the eyes of the man next to her who placed a gentle kiss on her lips.

She smiled knowing that she was no longer alone and that John would always be there for her. He was a part of her now. Part of him would always be with her.

Fin…

Was that okay? It was just something that came to mind. Does it need anything else? Please review.

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